Gene. 120 (1992) 291-295 0 1992 Elsevier Science Publishers
GENE
B.V. All rights reserved.
291
0378-l 119/92/%05.00
06698
Cloning, expression and tissue distribution fibroblast growth factor receptor subtype 4
of the
gene
encoding
rat
(Intracellular receptor; lung cDNA; molecular sequence data; polymerase chain reaction; protein-tyrosine kinase)
Robert A. Horlick,
Sylvia L. Stack and Gary M. Cooke
The Du Pont Merck Pharmaceutical Co., P.O. Box 80400. Experimental Station, Wilmington, DE 19880-0400. USA. Tel. (302) 695-7247 Received
by W.P. Sisk: 30 March
1992; Revised/Accepted:
7 April/25
April 1992; Received
at publishers:
26 June 1992
SUMMARY
The rat homologue of the gene encoding the fibroblast growth factor receptor subtype 4 (FGFRI) was cloned from rat lung mRNA, and the cDNA sequence was found to be 95% similar and 92% identical to the human homologue. Northern blot analysis of adult rat tissues demonstrated that a 3.1-kb mRNA encoding FGFR4 is detectable only in the lung and kidney. The receptor variant described here encodes two potential immunoglobulin-like domains, 21 hydrophobic amino acids encoding a potential transmembrane domain, and a split tyrosine kinase motif. However, the acidic box and hydrophobic signal peptide domains are not present in this cDNA isolate.
INTRODUCTION
A family of receptors that binds acidic and basic fibroblast growth factor (aFGF and bFGF) and at least some members of the related family of FGF proto-oncogenes have recently been identified. The four receptor subtypes within this family that have been cloned and characterized include: FGFRl or JEg (Lee et al., 1989; Pasquale and Singer, 1989; Isacchi et al., 1990), FGFR2 or bek (Dionne et al., 1990; Houssaint et al., 1990), FGFR3 and cek2 (Pasquale, 1990; Keegan et al., 1991), and FGFR4 (Par&men
Correspondence to: Dr. R.A. Horlick, The DuPont
Merck
Pharmaceutical
USA. Tel. (302) 695-7247; Abbreviations:
E400/5225,
aa, amino acid(s); aFGF,
fibroblast growth factor; FGFR, FGF FGFR; h-, human; Ig, immunoglobulin;
acidic FGF; bFGF,
receptor; FGFR, gene encoding kb, kilobase or 1000 bp; nt,
oligo, oligodeoxyribonucleotide;
sulfate; TyrK, tyrosine
basic FGF;
to RNA; A, deletion; FGF,
ORF, open reading frame;
PCR, polymerase chain reaction; r-, rat; RACE, rapid cDNA ends; SSC, 0.15 M NaCl/O.OlS M Na,.citrate sodium dodecyl
Station,
DE 19880-0400,
Fax (302) 695-7054.
bp, base pair(s); cDNA, DNA complementary
nucleotide(s);
Experimental
Co., Wilmington,
kinase.
amplification of pH 7.6; SDS,
et al., 1991). These receptors belong to the protein TyrK as well as to the Ig-like superfamilies of hormone receptors. Members of this family characteristically contain a hydrophobic signal sequence, an acidic region, two or three Iglike domains, a single hydrophobic transmembrane domain, and a cytoplasmically located ‘split’ TyrK enzymatic moiety (Fig. 1). The mRNAs encoding FGFRl and FGFR2 are also known to include several alternatively spliced variants. In one alternatively spliced form, the most N-terminal of the three Ig-like domains is absent (Johnson et al., 1990; Mansukhani et al., 1990). Furthermore, there are known to be three alternative exons that can be used to encode the C-terminal half of the third Ig domain (Johnson et al., 1991). The choice of exon utilization in the third Ig domain can determine the ligand-binding specificity of the resulting receptor (Miki et al., 1992; Werner et al., 1992) and whether the receptor is anchored to the cell membrane or is secreted from the cell (Johnson et al., 1990). Finally, Hou et al. (1991) have reported a variant of FGFRl that they term the ‘ y N-terminal motif which contains no signal sequence or acidic box. We report here the cloning and characterization of the rat homologue of the FGFR4 receptor that, like the y N-terminal motif of FGFRl, lacks a signal sequence and acidic box.
292 -60
-10 .
. CATCAATAACGAGGACCCUCCTCAGCAGCTCCTCG t60 . . . . CGGGAAU\CTGmAAATTCCTGTCCAGCTGCAGGGAAC GNTVKFRCPAAGNPMPTIHWLKNGQAFHGENRIGGIRLRH T flS0 . . CCAACACTGGAGCCTCGTGATGGAGAGCGTGGTGCCCTCAG QHW S LV MESVVP S D R
.
.
t10 . . GCBTGGAUlAGAAACTGCACGCGGTACCTGC MEKKLHAVPA t120 .
.
.
D
R
+240 .
. GT
Y
TCLV
ENS A
L V
GS
. I
RY
S N
Y
LL
DVL
. . GTCCCCGCACCGGCCCATCCTGCAGGCGGWLCTCCCAGCCT SPHRPILQAGLPANTTAVVGSNVELLCKVYSDAQPHIQWLl30
D +4ao +420 . . . . . . . GAAGCACATCGTTATCAACGGCAGCAGTCTCGGCGCTGAT~TTTCCCCTACGTA~GTCCT~GA~~~~T~TA~T~~ffiT~~T~TGTATCT~~ffiTGTC KHIVINGSSLGADGFPYVQVLKTTDINSSEVEVLYLRNVS170 A P V +600 t540 . . . . . . . GGCTWLGGATGULCX;GGAGTACACCT~G~CTC~TC~CTCTCCTAC~GT~~GT~T~CAGT~TACCC~~~~~~CCTC~GT~~~~~C AEDAGEYTCLAGNSIGLSYQSAWLTVLPAEEEDLAWTTAT210 A A P T t720 +660 . . . . . . ATCGGRGGCCAWLTATACTATTATCCTATATGTCCAT~T~CT~TTT~TTTT~TCCT~T~T~C~TGTAT~CC~~~TC~C~~C~CTCTCGA~ SEARYTDIILYVHGSLALVLLLLLAGVYHRQAIHGHHSRQ250 L R L RG A S A v P +I340 t700
.
.
.
.
.
E
R
+360 .
+300
.
.
A
A
.
P
P
.
GCCTGTCACTGTACAWLAGCTGTCCCffiTTCCCTTTffiC~~GTTCT~TT~GTC~~TCCTCT~GT~GTTTGTCCCT~T~~~TGTCC~TCTCCTC~GT~
LVRGVRLSSSGZ90 S G C960 +920 . . . . . . . . CCW;CCCTTGCTCACGGGCCTTGTWLGTCTAGACCTACCTCTC~TC~CTTT~GTTCCCCC~~~TffiTGCTC~GCCCCT~T~~T~TTT~~GTffiT PPLLTGLVSLDLPLDPLWEFPRDRLVLGKPLGEGCFGQVV330 P;TVQKLSRFPLARQFSLESRSSGKSSLS
A
.
A
.
.
+1020
.
.
.
+1oao
.
.
TTGTGCAGAAGCCCTTGGCATGGATTCCTCCCGGCCAGAC-CCA~TCGT~TGT~~T~T~~~T~TCC~C~~ATTT~~CCT~TCTC~A~T~ CAEALGMDSSRPDQTSIVAVKMLKDNASDKDLADLISEME370 A T P A F P t1200 t1140
.
.
.
.
GATGATGAAGCTAATCGGAAGACATT~CCT~TG~TGTC~CTCA~~CCC~TATGTGATTGT~TATGC~~ MMKLIGRHKNIINLLGVCTQEGPLYVIVEYAAKGNLREFL410
.
. V
. . GXAAACCTTCGGGAATTCCT
C
V
+1320
t1260 . . . . CAGGCCCTGATCTCAGCCCTGATGGGCCTCGWLGCAGCGA CCGTGUXGGCGTCCCC RARRPPGPDLSPDGPRSSEGPLSFPALVSCAYQVARGMQY450
.
V +I380 . . . TCTGGAGTCTCGGAAGTGCRTCCACCGGGACCTGGCTGCC LESRKCIHRDLAARNVLVTEDDVMKIADFGLARGVHHiDY490
.
.
.
.
.
.
.
.
.
.
t1440 .
.
t1560
.
.
CTATAAGAAAACCAGCAATGGCCGCCTGCCAGTCAAGTM;T YKKTSNGRLPVKWMAPEALFDRVYTHQSDVWSFGILLWEI530 t1620 . . . . . TCW%ATACCCCGGCATCCCAGTGWLGGAGCn;TTCTCACTT CTTCACCCTCGGGGGC FTLGGSPYPGIPVEELFSLLREGHRMERPPNCPSELYGLM570
+16SO .
D +1740 . . . . . CTTTTAAGCAGCTGGTGGAAGCTCTGWLCAAGGTCCTGCT GAC&GAGTGTTGGCACGCACXTCCTTCTCAGAGGCCGA RECWHAAPSQRPTFKQLVEALDKVLLAVSEEYLDLRLTFG610
w +1eoo
+I860 +1920 . . . . . ACCCTATTCCCCCAACAATGT~~G~~ffiT~TCCTC~~CTCGGTTTT~GC~C~~CTTT~CC~~~~~C~TT~~TTTCCT~~A~C~C PYSPNNGDASSTCSSSDSVFSHDPLPLEPSPFPFPEAQTT650 SC OS 8 +19ao 1-2040 . . . . ~~CTGGGAACWLTGTTGCATGGGCTCGTA~CCGT~CGT~CTC~CCTGTTT~TCA~TTTGACGTT~CTGT~T~~CTCT~CTC~~TACT~T~
P
.
.
GSGVQ
l
t2100 t2160 . . . . . . . CCAGATCCTCTCTCTGGCCCTGTTTT~A~C~T~TTffiTCTT~TT~~GTT~~CTTCTGTTC-CTTATGTTC~~T~~GTT~CTCCTCGTCT~~T +2220 +22ao . . . . . . CATGGTCGTGCCCTTGGACTCATCCTCCT-~~~TT~~CTT~~CTTA~CT~CCC~~TCTC~CTGACT~TCTTT~TCCT~~TTTCTA~ +2340 t2400 . . . . . . . TCCCCAAACAACCTAGAGGCCTCGGGACTTCACTGULCCCCC~CCC~~C~~~CTC~CAC~T~TCCCC~CTCCC~CT~TTGTTCTA~TCTTGTT~~~CT t2460 +2520 . . . CAGCTCTGGTGTCCTTGAGAGAGGGAAGCCTGTGGAAAAW
. . .
293 EXPERIMENTAL
AND DISCUSSION
of r-FGFR4 cDNA Degenerate oligo primers were designed according to a reverse translation of the published aa sequence of the chicken fig FGFR subtype (Lee et al., 1989). Adult rat lung had been previously observed by 1251-autoradiography to contain very high concentrations of bFGF binding (William Herblin, unpublished observations). Therefore, mRNA from rat lung was used as the starting material for the synthesis of oligo(dT)-primed cDNA. One of the eleven pairs of degenerate oligo primers tested was able to amplify a 770-bp band that was subsequently cloned and sequenced. The computer-generated translation of the nt sequence ORF revealed several regions of aa homology to the chicken Jig sequence. Nondegenerate oligo primers were then made according to the sequence information obtained from the PCR-amplified band and were used to amplify the 5’ and 3’ ends of the cDNA using the RACE technique (Frohman et al., 1988). Three overlapping fragments representing the 5’, middle, and 3’ portions of the FGFR4 cDNA were thus obtained. At least two independent isolates were cloned and sequenced for each of these three fragments to control for the possibility of PCR-induced mutations. The three overlapping cDNA fragments were spliced into one contiguous fragment using the technique of PCRmediated assembly of overlapping DNA fragments (Ho et al., 1989; Horton et al., 1989) to yield a final assembled 2.7-kb cDNA. The first ATG codon appears at nt 92 and is followed by an ORF that encodes a 660-aa protein (Fig. 1) and ends with a TGA stop codon. The deduced protein contains a hydrophobic region of 21 aa (Ile228 to Tyr248) which resembles a transmembrane domain. While this work was in progress, the sequence of the human FGFR4 (BFGFR4) cDNA was published (Partanen et al., 1991). The nt and deduced aa sequences of h-FGFRI are 86% and 92% identical, respectively, to the sequences shown in Fig. 1. On the basis of this close ho-
(a) Cloning and characterization
kb 9.5 7.5
28s
-
4.4--
2.4 18s
-
i::
-
Fig. 2. Northern
blot analysis
of various
Total RNA (10 ng) was isolated Sprague-Dawley
rats) and resolved
rose gel (Sambrook position
of 28s and 18s ribosomal
sulfate/40%
Ficoll, and 20 pg of sheared out overnight
salmon
formamide/
Madison,
represent
WI) consisting
nylon
membranes
at 42°C for 5 h
serum
albumin/0.04%
sperm DNA per ml. Hybridization
in the same solution containing
1.5 x IO5 cpm/
System kit, Promega,
of the 5’ terminal 721 nt of the r-FGFR4
twice for 5 min at room temperature after a 2-week exposure
clone.
in 2 x SSCjO. 1%
SDS and twice for 30 min at 55°C in 0.1 x SSC/O.l% iogram was developed
agakb) and
x SSC/7 mM Tris pH
bovine
ml of a 32P-labeled DNA fragment (Nick Translation Blot was washed
Methods.
(300 g male
are labeled at the left side of
to GeneScreenm
polyvinyl-pyrrolidone/O.O4%
was carried
(numbers
and the blot was prehybridized
in 40 ml of 10% dextran 7.6/0.04x
RNAs
were transferred
Nuclear),
rat tissues
on a 2.2 M formaldehyde-1.2%
et al., 1989). Size markers
the figure. RNAs (New England
rat tissue mRNAs.
from various
SDS. Autorad-
at -80°C.
mology, the lung isolate appears to be the rat homologue of the h-FGFRI sequence. However, the cDNA sequence described here does not encode a hydrophobic signal se-
Fig. 1. The nt sequence of the rat lung cDNA isolate, r-FGFR4, and the deduced aa sequence. Numbers and dots above every line refer to nt numbers; aa are aligned with the lirst nt of each codon, and numbers are marked at the end of each line. The putative ATG start and stop codons are underlined. The postulated
transmembrane
found in the h-FGFRI sequence.
domain
is shown with double underlining.
gene that differ from the rat sequence.
Methods. Rat lung poly(A)+mRNA
was reverse transcribed
cDNA was made from 0.2 pg methyl mercury-denatured passed
over a Linkers
5 column
(5 Prime-3
gene (Lee et al., 1989) was performed (the coding potential
for aa EMEMMKMI,
represent
letters shown below the rat aa sequence aa residues
from Invitrogen.
using the oligo TTCTCGAGAATTCTAGA(T,,).
Prime), diluted to 500 ~1, and boiled for 5 min. A reverse translation programs
(containing
(Devereux
for aa DPQPHIQW)
the residues
relative to the rat
Briefly, single-stranded
The cDNA-RNA of the aa sequence
et al., 1984) and was used to design degenerate
the coding potential
represent
that are deleted from the human
using the Red Module kita and protocol
poly(A)+RNA
using the Wisconsin
primers 5’-GAYCCNCARCCNCAYATHCARTGG
The boldfaced
The A symbols
hybrid was
of the chicken Jig
oligo primers.
The oligo
and 5’-ATCATYTTCATCAMCCAMC
where Y = C or T; R = A or G; N = A, C, G or T; and H = A,C or T) were used to amplify the initial 770-
bp receptor fragment. PCR reactions were generally carried out at 94°C for 1 min, primer annealing temperature for 1 mm, and 72°C for 3 min for 29 cycles followed by a 7 min chase at 72°C. The primer annealing temperature was calculated as described by Sambrook et al. (1989). An annealing temperature of 55°C was used for the degenerate oligos. All sequencing reactions were performed using Sequenase Version 2.0 sequencing kit from US Biochemical (Cleveland, OH) following the protocol provided. The 5’ and 3’ ends of the rat FGFR4 cDNA were amplified essentially as described by Frohman
et al. (1988). This sequence
has been deposited
in the GenBank
database
under accession
No. M91599.
294 quence, the acidic box characteristic of the FGFR members, and the first Ig domain, as described for the human version (Partanen et al., 1991.) (b) Tissue-specific expression of r-FGFR4 The expression of the r-FGFR4 gene was determined using Northern blot analysis of the total RNA isolated from various rat tissues. Using the region of the cDNA encompassing the putative extracellular domain (nt -50 to + 671 as shown in Fig. 1) as a hybridization probe, a RNA species of approximately 3.0-3.2 kb was detected in the lung and kidney (Fig. 2). The identity of the faintly hybridizing band at approx. 4.2 kb observed in the spleen is unknown but may be due to an alternatively spliced version of the r-FGFR4 mRNA, use of an alternative poly(A)’ signal, or possibly cross-hybridization to another related FGFR subtype. No hybridizing mRNA species were detectable in any of the other tissues analyzed: liver, brain, testes, heart, fat pads, stomach, or intestines. The tissue-specific pattern of expression observed in Fig. 2 differs considerably from the pattern shown by Partanen et al. (1991). These authors observed expression of FGFR4 in many tissues including the liver, spleen, and intestine which are not detectable on the autoradiogram shown in Fig. 2. This might be explained, however, by the fact that the Northern blot mRNA samples used by Partanen et al. (1991) were obtained from 17-18-week-old human fetuses, whereas the samples used in Fig. 2 were obtained from adult rat tissues and organs.
(3) Intriguingly, analogous forms of cDNAs encoding the Jig (termed the ‘ y N-terminal motif in Hou et al., 1991) and the bek (A. Yayon, personal communication) FGF
receptor subtypes have been observed in which initiation presumably begins at the first Met encountered, 16 aa Nterminal to the Cys residue that delineates the beginning of the second Ig domain (Met’ in Fig. 1). Like the y N-terminal motif of Hou et al. (1991), the isolate described in this work may therefore represent a potential intracellular form of the FGFR4 receptor. Studies are now underway to investigate further the subcellular localization of FGFR4 in the lung and kidney to test this hypothesis.
ACKNOWLEDGEMENTS
We wish to thank Donna Pedicord for her kind gift of the rat tissue RNAs and Northern blot used in the tissue distribution analysis, and William Herblin, Janet L. Dzubow, and Kristie Eidsvoog for helpful discussions, encouragement, and impetus for carrying out these studies.
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